Key message. This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. Abstract: The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their efects, and genetic and environmental interactions will facilitate plant breeders manipulating fowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major fowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL efects, interactions between genes and with the environment are presented. Pleiotropic efects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large efects on phenology that became relevant in modern barley breeding. The parallelisms between fowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic efects that provide enormous plasticity in barley fowering behavior, which opens new avenues to breeders for fne-tuning phenology of the barley crop., Funding This research was supported by the contract “Iberia region hybrid barley variety development and understanding efects of adaptation genes in hybrids”, between CSIC and Syngenta Crop Protection AG, which included funding for MFC PhD scholarship, and by grants AGL2016-80967-R and PID2019-111621RB-I00 (Ministry of Science and Innovation of Spain), SUSCROP ERA-NET project BARISTA, PCI2019-103758, and the Government of Aragón (group A08_20R).

Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka × Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL co-locating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley., This work was supported by the Spanish Ministry of Economy and Competitiveness (grant numbers AGL2010-21929 and AGL2013-48756-R), the Spanish Ministry of Economy and Competitiveness, the Agencia Estatal de Investigación, and the European Regional Development Fund (grant number AGL2016–80967-R), and Government of Aragon (Research Group A08_20R).

Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka × Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL co-locating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley., This work was supported by the Spanish Ministry of Economy and Competitiveness (grant numbers AGL2010-21929 and AGL2013-48756-R), the Spanish Ministry of Economy and Competitiveness, the Agencia Estatal de Investigación, and the European Regional Development Fund (grant number AGL2016–80967-R), and Government of Aragon (Research Group A08_20R).

Key message. This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. Abstract: The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their efects, and genetic and environmental interactions will facilitate plant breeders manipulating fowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major fowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL efects, interactions between genes and with the environment are presented. Pleiotropic efects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large efects on phenology that became relevant in modern barley breeding. The parallelisms between fowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic efects that provide enormous plasticity in barley fowering behavior, which opens new avenues to breeders for fne-tuning phenology of the barley crop., Funding This research was supported by the contract “Iberia region hybrid barley variety development and understanding efects of adaptation genes in hybrids”, between CSIC and Syngenta Crop Protection AG, which included funding for MFC PhD scholarship, and by grants AGL2016-80967-R and PID2019-111621RB-I00 (Ministry of Science and Innovation of Spain), SUSCROP ERA-NET project BARISTA, PCI2019-103758, and the Government of Aragón (group A08_20R).

The dataset contains 1) bibliographic data from all published literature on genetic association (GWAS) in barley; 2) methodological data on procedures of analysis, traits analyzed, size of genotypic and molecular marker panels; 3) marker and trait information, including genome position (physical and genetic), extracted by the authors from the articles and from the barley reference genome sequence. The set of 144 articles were downloaded from the Web of Science and Scopus databases using appropriate keywords, and selected after inspection by the authors., © The Authors. Creative Commons License Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)., Dataset summarizing procedures and main findings of all studies to date devoted to genome-wide association studies in barley., Funding from grant “Descubrimiento y aplicación de QTL, genes y caracteres para la mejora genética de la cebada. Mecanismos de adaptación al clima”. Funding agency: MINECO, AGL2016-80967-R, Plan Nacional I+D+I (Ciencias Agrarias). Ernesto Igartua Arregui – Ana Mª Casas Cendoya., Peer reviewed

[Background] In winter barley plants, vernalization and photoperiod cues have to be integrated to promote flowering. Plant development and expression of different flowering promoter (HvVRN1, HvCO2, PPD-H1, HvFT1, HvFT3) and repressor (HvVRN2, HvCO9 and HvOS2) genes were evaluated in two winter barley varieties under: (1) natural increasing photoperiod, without vernalization, and (2) under short day conditions in three insufficient vernalization treatments. These challenging conditions were chosen to capture non-optimal and natural responses, representative of those experienced in the Mediterranean area., [Results] In absence of vernalization and under increasing photoperiods, HvVRN2 expression increased with day-length, mainly between 12 and 13 h photoperiods in our latitudes. The flowering promoter gene in short days, HvFT3, was only expressed after receiving induction of cold or plant age, which was associated with low transcript levels of HvVRN2 and HvOS2. Under the sub-optimal conditions here described, great differences in development were found between the two winter barley varieties used in the study. Delayed development in ‘Barberousse’ was associated with increased expression levels of HvOS2. Novel variation for HvCO9 and HvOS2 is reported and might explain such differences., [Conclusions] The balance between the expression of flowering promoters and repressor genes regulates the promotion towards flowering or the maintenance of the vegetative state. HvOS2, an ortholog of FLC, appears as a strong candidate to mediate in the vernalization response of barley. Natural variation found would help to exploit the plasticity in development to obtain better-adapted varieties for current and future climate conditions., Study financially supported by the Spanish Ministry of Economy, Industry and Competitiveness (Projects AGL2013–48756-R, including a scholarship granted to AM, and AGL2016–80967-R). The funding body did not play any role in the design of the study, collection, analysis, interpretation of the data or in writing the manuscript. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

51 Pags.- 4 Tabls.- 6 Figs. © 2019 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. The definitive version is available at: https://onlinelibrary.wiley.com/journal/1365294x, Landraces are local populations of crop plants adapted to a particular environment. Extant landraces are surviving genetic archives, keeping signatures of the selection processes experienced by them until settling in their current niches. This study intends to establish relationships between genetic diversity of barley (Hordeum vulgare L.) landraces collected in Spain and the climate of their collection sites. A high‐resolution climatic data set (5 × 5 km spatial, 1‐day temporal grid) was computed from over 2,000 temperature and 7,000 precipitation stations across peninsular Spain. This data set, spanning the period 1981–2010, was used to derive agroclimatic variables meaningful for cereal production at the collection sites of 135 barley landraces. Variables summarize temperature, precipitation, evapotranspiration, potential vernalization and frost probability at different times of the year and time scales (season and month). SNP genotyping of the landraces was carried out combining Illumina Infinium assays and genotyping‐by‐sequencing, yielding 9,920 biallelic markers (7,479 with position on the barley reference genome). The association of these SNPs with agroclimatic variables was analysed at two levels of genetic diversity, with and without taking into account population structure. The whole data sets and analysis pipelines are documented and available at https://eead-csic-compbio.github.io/barley-agroclimatic-association. We found differential adaptation of the germplasm groups identified to be dominated by reactions to cold temperature and late‐season frost occurrence, as well as to water availability. Several significant associations pointing at specific adaptations to agroclimatic features related to temperature and water availability were observed, and candidate genes underlying some of the main regions are proposed., This work was supported by the FACCE ERA-NET Plus project ClimBar (618105) and by Spanish Agencia Estatal de Investigación projects CGL2014-52135-C3-3-R, AGL2013-48756-R, AGL2016-80967-R and RFP2015-00006-00-00. BCM was funded by Fundación ARAID., Peer reviewed

14 Pags.- Figs.- Fots. Copia de la presentación expuesta (Comunicación oral) por la primera autora en el II Spanish Symposium on Cereal Physiology and Breeding of Cereals. Este simposio fue organizado por el Rectorado de la Universidad de Córdoba (UCO) como parte de las actividades de la Red de Excelencia científica «Fisiología del Rendimiento y Calidad para la Mejora de Cereales» (FiRCMe). http://sefimec.csic.es/ Under Creative Commons License Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)., The Spanish Barley Core Collection (SBCC) presents a wide range of adaptation traits to Mediterranean environments. Some of the SBCC lines have shown good performance in low productivity sites and, thus, they could be good candidates to introgress drought adaptation to commercial cultivars. To that purpose, two backcross populations (BC2F5) were developed using two SBCC landraces (SBCC042 and SBCC073) as donor parents and the elite cultivar Cierzo as recurrent parent. Genotyping of 264 lines of each backcross was carried out using the Barley Illumina iSelect 50k SNPchip, which provided a good genome coverage for both populations. We carried out three years of field trials, in Zaragoza (Spain), the last one of them used for QTL validation. The use of two distinct populations led us to find interesting hotspots. Among them, QTL for test weight and kernel weight open the possibility of exploiting the Spanish landraces as source of variability for agronomic and quality traits.
On chromosome 1H, we found a region in 503 – 526 Mb, which involved flowering time, kernel weight and test weight, co-locating with the locus Thresh-1 (threshability1) and an arabinoxylan content QTL2. In addition, a plant height and kernel weight QTL on 5H coincided with a region for grain plumpness reported in the literature3. Another important region was found on 6H, related with yield and quality traits. The confidence interval of this hotspot covered a long extension of the chromosome, overlapping yield, height and kernel weight. For this QTL region, lower productivity was concurrent with taller plants and heavier kernels, all contributed by the landrace allele. Strategies to use the QTL found for breeding and pre-breeding purposes will be discussed., This work was supported by Spanish Ministry of Economy, Industry and Competitiveness grants AGL2013-48756-R, AGL2016-80967-R, RFP2012-00015-00-00, RFP2015 00006-00-00, and RTA2012-00033-C03-02. AM was funded by the Spanish Ministry of Economy, Industry and Competitiveness grant no. BES-2014-069266 (linked to project AGL2013-48756-R)., Peer reviewed

17 Pags.- 3 Figs.- 2 Tabls. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license., Early vigor has been proposed as a favorable trait for cereals grown in drought-prone
environments. This research aimed at characterizing early stage shoot and root growth of three
Spanish barley landraces compared with three modern cultivars. Genotypes were grown in an
automated phenotyping platform, GrowScreen-Rhizo, under well-watered and drought conditions.
Seminal and lateral root length, root system width and depth were recorded automatically during
the experiment. Drought induced greater growth reduction in shoots (43% dry weight reduction)
than in roots (23% dry weight). Genotypic differences were larger under no stress, partly due to a
more profuse growth of landraces in this treatment. Accession SBCC146 was the most vigorous for
shoot growth, whereas SBCC073 diverted more assimilates to root growth. Among cultivars, Cierzo
was the most vigorous one and Scarlett had the least root dry weight of all genotypes, under both
conditions. Root growth was redirected to lateral roots when seminal roots could not progress further
in dry soil. This study reveals the presence of genetic diversity in dynamics of early growth of barley.
The different patterns of growth observed for SBCC073 and SBCC146 should be explored further, to
test if they affect field performance of barley in drought-prone environments., This research was supported by the Transnational Access capacities of the European Plant Phenotyping
Network (EPPN, grant agreement no. 284443) funded by the FP7 Research Infrastructure Programme of the
European Union, and by the Spanish Ministry of Science and Competitiveness (MINECO, including FEDER
funds) projects AGL2013-487656-R, AGL2016-80967-R and and RFP2012 00015-00-00. RB was supported by a
scholarship from CIHEAM, and from a travel grant (Chercheurs en formation a l’étranger) from the Ministry of
Higher Education and Scientific Research of Algeria., Peer reviewed

© 2020 by the authors., Seminal roots are known to play an important role in crop performance, particularly under drought conditions. A set of 37 durum wheat cultivars and local landraces was screened for variation in architecture and size of seminal roots using a laboratory setting, with a filter paper method combined with image processing by SmartRoot software. Significant genetic variability was detected for all root and shoot traits assessed. Four rooting patterns were identified, with landraces showing overall steeper angle and higher root length, in comparison with cultivars, which presented a wider root angle and shorter root length. Some traits revealed trends dependent on the genotypes’ year of release, like increased seminal root angle and reduced root size (length, surface, and volume) over time. We confirm the presence of a remarkable diversity of root traits in durum wheat whose relationship with adult root features and agronomic performance should be explored., This study was funded by University of Alcalá Project CCGP2017-EXP/007. E.I. and A.M.C. acknowledge funding from the Spanish Ministry of Economy and Competitiveness and the Agencia Estatal de Investigación (Project AGL2016–80967-R), and the European Regional Development Fund., Peer reviewed

3 Pags.- 2 Figs. This is an open access article distributed under the terms of the Creative Commons CC BY license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited., Dixon et al. (2020) report a novel role for the TB1 transcription factor gene in wheat, controlling plant height. This gene and its orthologues have long been known to affect branching in a number of crops and plant species. Its involvement in the determination of plant height opens up new avenues for the modification of this key trait, which affects multiple agronomic aspects of annual crops, from emergence to harvest index., The authors receive strategic funding from the Government of Aragón,
research group A08-17R, the Spanish Ministry of Science and Innovation
[AGL2016-80967-R], the UK Biosciences and Biotechnology Research
Council [BB/P016855/1], the National Sciences Foundation [1127112],
and the European Molecular Biology Laboratory., Peer reviewed

31 Pags.- 4 Figs.- 6 Tabls. © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made., The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop., This research was supported by the contract “Iberia region hybrid barley variety development and understanding effects of adaptation genes in hybrids”, between CSIC and Syngenta Crop Protection AG, which included funding for MFC PhD scholarship, and by grants AGL2016-80967-R and PID2019-111621RB-I00 (Ministry of Science and Innovation of Spain), SUSCROP ERA-NET project BARISTA, PCI2019-103758, and the Government of Aragón (group A08_20R)., Peer reviewed

11 Pags.- 3 Figs.- 3 Tabls. © 2021 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.This is an open access article under the CC BY-NC-ND license, Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant’s response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka × Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL co-locating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley., This work was supported by the Spanish Ministry of Economy and Competitiveness (grant numbers AGL2010-21929 and AGL2013-48756-R), the Spanish Ministry of Economy and Competitiveness, the Agencia Estatal de Investigación, and the European Regional Development Fund (grant number AGL2016–80967-R), and Government of Aragon (Research Group A08_20R)., Peer reviewed

[EN] This Excel file contains the raw data of the experiment reported in the article “Responses of Barley to High Ambient Temperature Are Modulated by Vernalization”, published in Frontiers in Plant Science, and referenced as Supplementary Table 7. Data are phenological development variables and yield-related variables for eight genotypes of barley grown in growth chambers, under four treatments combining presence/absence of vernalization and normal/high temperatures == [ES] Archivo excel con los datos de un experimento incluido en la publicación Ochagavía et al., en Frontiers in Plant Science. La primera hoja contiene la explicación de los datos, recogidos en la segunda hoja del archivo., Raw data (Supplementary Table 7) of article by Ochagavía et al., published in Frontiers in Plant Science., Funding of this research was provided was provided by
project AGL2016-80967-R (Agencia Estatal de Investigación,
Ministry of Economy and Competitiveness), project PID2019-
111621RB-I00 (Agencia Estatal de Investigación), grants
A08_17R and A08_20R (Government of Aragón), and project
GINOP-2.3.2-15-2016-00029 (Economic Development Programs
of the Hungarian Ministry of Finance)., Peer reviewed

14 Pags.- 4 Figs.- 3 Tabls.- Data availability: The sequence reads generated for this study can be found in the European Nucleotide Archive (ENA) at https://www.ebi.ac.uk/ena/browser/view/PRJEB35759, Light quality influence on barley development is poorly understood. We exposed three barley genotypes with either sensitive or insensitive response to two light sources producing different light spectra, fluorescent bulbs, and metal halide lamps, keeping constant light intensity, duration, and temperature. Through RNA-seq, we identified the main genes and pathways involved in the genotypic responses. A first analysis identified genotypic differences in gene expression of development-related genes, including photoreceptors and flowering time genes. Genes from the vernalization pathway of light quality-sensitive genotypes were affected by fluorescent light. In particular, vernalization-related repressors reacted differently: HvVRN2 did not experience relevant changes, whereas HvOS2 expression increased under fluorescent light. To identify the genes primarily related to light quality responses, and avoid the confounding effect of plant developmental stage, genes influenced by development were masked in a second analysis. Quantitative expression levels of PPD-H1, which influenced HvVRN1 and HvFT1, explained genotypic differences in development. Upstream mechanisms (light signaling and circadian clock) were also altered, but no specific genes linking photoreceptors and the photoperiod pathway were identified. The variety of light-quality sensitivities reveals the presence of possible mechanisms of adaptation of winter and facultative barley to latitudinal variation in light quality, which deserves further research., This work was supported by the Spanish Ministry of Economy and Competitiveness (Projects AGL2013-48756-R, including scholarship BES-2014-069266, granted to AM, and AGL2016-80967-R), Agencia Estatal de Investigación of the Spanish Ministry of Science and Innovation (PID2019-111621RB-I00), and Department of Innovation, Research and Universities of the Government of Aragon (A08-20R). The contribution of the Hungarian partners was funded by a research grant from the National Research, Development and Innovation Office (NKFIH-FK-134234) and the János Bolyai Research Scholarship of TK from the Hungarian Academy of Sciences (BO/00396/21/4), Peer reviewed

9 Pags.- 3 Figs.- 1 Tabl. Data availability statement: The exome capture dataset utilized in this study is available at the European Nucleotide Archive, accession PRJEB73755. © 2024 Cabeza, Casas, Larruy, Costar, Martínez, Contreras-Moreira and Igartua. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY)., The process of allocating resources to different plant organs in the early stage of development can affect their adaptation to drought conditions, by influencing water uptake, transpiration, photosynthesis, and carbon storage. Early barley development can affect the response to drought conditions and mitigate yield losses. A distinct behavior of biomass partitioning between two Spanish barley landraces (SBCC073 and SBCC146) was observed in a previous rhizotron experiment. An RIL population of approximately 200 lines, derived from the cross of those lines, was advanced using speed breeding. We devised an experiment to test if seedling biomass partitioning was under genetic control, growing the seedlings in pots filled with silica sand, in a growth chamber under controlled conditions. After 1 week, the shoot and root were separated, oven dried, and weighted. There were genotypic differences for shoot dry weight, root dry weight, and root-to-shoot ratio. The population was genotyped with a commercial 15k SNP chip, and a genetic map was constructed with 1,353 SNP markers. A QTL analysis revealed no QTL for shoot or root dry weight. However, a clear single QTL for biomass partitioning (RatioRS) was found, in the long arm of chromosome 5H. By exploring the high-confidence genes in the region surrounding the QTL peak, five genes with missense mutations between SBCC146 and SBCC073, and differential expression in roots compared to other organs, were identified. We provide evidence of five promising candidate genes with a role in biomass partitioning that deserve further research., The author(s) declare financial support was received for the research, authorship, and/or publication of this article. Funding of this research was provided by project AGL2016-80967-R (MINECO/AEI) 10.13039/501100011033 and by “ERDF A way of making Europe,” project PID2019-111621RB-I00 (MCIN/AEI) 10.13039/501100011033, project PID2022-142116OB-I00 (MCIN/AEI) 10.13039/501100011033, and by “ERDF A way of making Europe,” grant A08_23R (Government of Aragón). Computing hardware was funded by grant FAS2022_052 from CSIC. AC was supported by the FPI grant BES-2017-082746 (MCIN/AEI) 10.13039/501100011033, and by “ESF investing in your future.”, Peer reviewed

288 Pags.- Figs.- Tabls. Tesis doctoral Universidad de Lleida, Programa de Doctorado en Ciencia y Tecnología Agraria y Alimentaria, realizada en la Estación Experimental de Aula Dei (EEAD-CSIC)., [ES] Actualmente, la reducción y la incertidumbre de las precipitaciones han situado la tolerancia a la sequía como uno de los principales objetivos de la mejora vegetal para la agricultura de secano en España y en toda la región mediterránea. Las raíces han sido la mitad oculta de la investigación vegetal y no han recibido suficiente atención en el pasado. Recientemente, se han desarrollado varios métodos para el fenotipado de raíces. En esta tesis, hemos estudiado el método de rhizoslides para estudiar la arquitectura del sistema radicular (RSA). Este método se probó en una población biparental de cebada de élite, Orria x Plaisant, encontrando diversidad genética y QTL para la mayoría de rasgos. Las líneas extremas para el ángulo de apertura de la raíz (RoA) se probaron posteriormente para la estructura de la raíz en condiciones de campo. Un análisis multifactorial que combinaba los caracteres agronómicos disponibles anteriormente con los dos análisis de raíces encontró una correlación negativa entre el RoA en el estadio de plántula y el peso de mil granos (TKW) en todos los años y localizaciones probados. Para las raíces adultas, una RSA estrecha, compacta, con un crecimiento radicular profuso fue ventajosa para el rendimiento en los ensayos de campo que sufrieron más sequía. Se detectaron algunos QTL para rasgos de raíz en el estadio de plántula y algunos de ellos se localizaron con QTL de rendimiento o rasgos de cosecha relacionados. Estudiar y definir los principales rasgos de la RSA en el estadio de plántula podría ser un posible indicador para predecir el rendimiento agronómico y para seleccionar con antelación genotipos con una mayor capacidad para adquirir agua de las capas de suelo más profundas.

Explorar y utilizar la diversidad genética de las variedades antiguas de cebada, que llevaban adaptación a la sequía, podría conducir a plantas más resistentes a la sequía. Las variedades locales de la Colección Española de Cebada son interesantes para la mejora vegetal en España debido a su diversidad genética inexplorada. Se cruzaron dos líneas representativas de esta colección para crear una población de líneas endogámicas recombinantes (RIL), avanzada mediante la metodología de speed breeding. La población se evaluó en cinco experimentos de campo. Los dos más grandes experimentaron sequía (terminal en VED22, severa y prolongada en VED23) durante la temporada. Además, se cuantificaron los rasgos de cobertura vegetal (Área Verde, Índice de Senescencia de la Cosecha, NDVI) en dos ensayos, utilizando imágenes RGB y Greenseeker. El rendimiento en VED23 fue mucho inferior al de VED22. No obstante, esta reducción se atribuyó a componentes del rendimiento determinados más tarde en el ciclo (número de granos por espiga o TKW), más que a los determinados antes, como el número de tallos y espigas. Los rasgos decoberturavegetal fueronpredictivos,en cierta medida, parael rendimiento del grano. Se encontraron 59 QTL, situados a lo largo de todos los cromosomas excepto el 6H, agrupados en 30 regiones. Se detectó una zona de concentración de QTL en el 7H, que correspondía al gen HvFT1.

La población SBCC073 x SBCC146 también se sometió a una prueba de partición de biomasa entre raíces y tallos, en plántulas. Estudios previosmostraronuna cantidad diferente de asignación de biomasa en estas dos líneas, con SBCC073 presentando una mayor biomasa de raíz en comparación con SBCC146, que dedicó más recursos de carbono a la parte aérea. Probamos la población RIL y los padres, y encontramos una amplia diversidad genotípica para el peso seco de la raíz, el peso seco del tallo y la relación raíz-tallo (RatioRS). Se detectó un solo QTL para RatioRS, en el cromosoma 5H. Explorando los genes de alta confianza con datos de captura de exoma en la región que rodea el pico del QTL, se identificaron cinco genes con mutaciones de cambiode sentido entreSBCC146 y SBCC073, y expresión diferencial en raíces en comparación con otros órganos., [CA] Actualment, la reducció i la incertesa de les precipitacions han situat la tolerància a la sequera com un dels principals objectius de la millora vegetal per a l’agricultura de secà a Espanya, i a tota la regió mediterrània. Les arrels han estat la meitat oculta de la recerca vegetal, i no han rebut prou atenció en el passat. Recentment, s’han desenvolupat diversos mètodes per al fenotipatge d’arrels. En aquesta tesi, hem estudiat el mètode del rhizoslides per a estudiar l’arquitectura del sistema radicular (RSA). Aquest mètode es va provar en una població biparental d’ordi d’elit, Orria x Plaisant, trobant diversitat genètica i QTL per a la majoria de trets. Les línies extremes per a l’angle d’obertura de l’arrel (RoA) es van provar posteriorment per a l’estructura de l’arrel en condicions de camp. Una anàlisi multifactorial que combinava els caràcters agronòmics disponibles anteriorment amb les dues anàlisis d’arrels va trobar una correlació negativa entre el RoA en l’estadi de plàntula i el pes de mil grans (TKW) en tots els anys i localitzacions provats. Per a les arrels adultes, una RSA estreta, compacta, amb un creixement radicular profús va ser avantatjosa per al rendiment en els assajos de camp que van patir més sequera. Alguns QTL van ser detectats per a trets d’arrel en l’estadi de plàntula i alguns d’ells es van col·locar amb el rendiment o trets de relacionats amb la collita. Estudiar i definir els principals trets de la RSA en l’estadi de plàntula podria ser un possible indicador per a predir el rendiment agronòmic i per a seleccionar amb antelació genotips amb una major capacitat per a adquirir aigua de les capes de sòl més profundes.

Explorar i utilitzar la diversitat genètica de les varietats antigues d’ordi, que portaven adaptació a la sequera, podria conduir a plantes més resistents a la sequera. Les varietats locals de la Col·lecció Espanyola d’Ordi són interessants per a la millora vegetal a Espanya degut a la seva diversitat genètica inexplorada. Dues línies representatives d’aquesta col·lecció van ser creuades per a crear una població de línies endogàmiques recombinants (RIL), avançada mitjançant la metodologia de speed breeding. La població es va avaluar en cinc experiments de camp. Els dos més grans van experimentar sequera (terminal en VED22, severa i prolongada en VED23) durant la temporada. A més, es van quantificar els trets de la coberta vegetal (Àrea Verda, Índex de Senescència del Cultiu, NDVI) en dos assajos, utilitzant imatges RGB i Greenseeker. El rendiment en VED23 va ser molt inferior al de VED22. No obstant això, aquesta reducció es va atribuir a components del rendiment determinats més tard en el cicle (nombre de grans per espiga o TKW), més que als determinats abans, com el nombre de tiges i espigues. Els trets de la coberta vegetal van ser predictius, en certa mesura, per al rendiment del gra. Es van trobar 59 QTL, situats al llarg de tots els cromosomes excepte el 6H, agrupats en 30 regions. Es va detectar una zona de concentració de QTL al 7H, que corresponia al gen HvFT1.

La població SBCC073 xSBCC146 també es va provar per a la partició de la biomassa entre arrels i tiges en plàntules. Estudis previs van mostrar diferent quantitat de distribuciódebiomassa en aquestesdueslínies,amb SBCC073 presentant unamajor biomassa radicular en comparació amb SBCC146, que va dedicar més recursos de carboni a la part aèria. Vam provar la població RIL i els parentals, i vam trobar una àmplia diversitat genotípica per al pes sec de l’arrel, el pes sec de la tija i la relació arrel-tija (RatioRS). Es va detectar un sol QTL per a RatioRS, al cromosoma 5H. Explorant els gens d’alta confiança amb dades de captura d’exoma en la regió que envolta el pic del QTL, es van identificar cinc gens amb mutacions de canvi de sentit entre SBCC146 i SBCC073, i expressió diferencial en arrels en comparació amb altres òrgans., [EN] Currently, rainfall reduction and uncertainty have put drought tolerance at the forefront of plant breeding targets for dryland agriculture in Spain, and in the entire Mediterranean region. Roots have been the hidden half of plant research and have not received enough attention in the past. Recently, several methods for root phenotyping have been developed. In this thesis, we studied the rhizoslides’ method to study root system architecture (RSA). This method was tested in an elite barley biparental population, Orria x Plaisant, finding genetic diversity and QTL for most traits. The extreme lines for root opening angle (RoA) were further tested for root structure in field conditions. A multifactorial analysis combining previously available agronomic characters with the two root analyses found a negative correlation between RoA at seedling stage and thousand kernel weight (TKW) in all years and locations tested. For adult roots, a narrow RSA, compact,with profuseroot growth was advantageous for yield in the field trials that suffered more drought. Some QTL were detected forroot traits at seedlingstage and some ofthem co-located with yield or related harvest traits. Studying and defining main RSA traits at seedling stage could be a potential proxy to predict agronomic performance and to select in advance genotypes with enhanced ability to acquire water from deeper soil layers.

Exploring and utilizing the genetic diversity of ancient barley varieties, which carried adaptation to drought could led to more drought resilient plants. Landraces from the Spanish Barley Core Collection are interesting for breeding in Spain due to their untapped genetic diversity. Two lines representative of this collection were crossed to create a recombinant inbred line (RIL) population, advanced using speed breeding methodology. The population was evaluated in five field experiments. The two largest ones experienced drought (terminal in VED22, severe and extended in VED23) during the season. Moreover, canopy traits (Green Area, Crop Senescence Index, NDVI) were quantified in two trials, using RGB pictures and Greenseeker. Yield in VED23 was much lower than in VED22. However, this reduction was attributed to yield components determined later in the cycle (number of grains per spike or TKW), rather than those determined earlier, such as the number of stems and spikes. Canopycover traitswere predictive,to some extent,forgrainyield. Fifty-nine QTL, located along all chromosomes except 6H were found, grouped in 30 regions. A QTL hotspot was detected on 7H, corresponding to the HvFT1 gene.

The SBCC073 x SBCC146 population was also tested for biomass partitioning between roots and shoots in seedlings. Previous studies showed different amount of biomass allocation in these two lines, with SBCC073 presenting higher root biomass compared to SBCC146, which devoted more carbon resources to the aerial part. We tested the RIL population and the parents, and found wide genotypic diversity for root dry weight, shoot dry weight and root to shoot ratio (RatioRS). One single QTL was detected for RatioRS, on chromosome 5H. Exploring the high confidence genes with exome capture data in the region surrounding the QTL peak, five genes with missense mutations between SBCC146 and SBCC073, and differential expression in roots compared to other organs, were identified., Gracias al Ministerio de Ciencia, Innovación y Universidades por el contrato predoctoral para la formación de doctores/as FPI2017 (BES-2017-082746) financiada por MCIN/AEI/ 10.13039/501100011033 y por “FSE Invierte en tu futuro”. Gracias por el apoyo económico del proyecto AGL2016-80967-R financiado por MINECO/AEI 10.13039/501100011033 y por FEDER Una manera de hacer Europa. Gracias por el apoyo económico de los proyectos PID2019-111621RB-I00 y PID2022-142116OB-I00 fianciado por (MCIN/AEI) 10.13039/501100011033 y por FEDER Una manera de hacer Europa. Gracias por el apoyo económico del proyecto A08_23R del Gobierno de Aragón., Peer reviewed

18 Pags.- 6 Figs.- 2 Tabls. Data availability: All sequencing reads are available under study no. PRJEB85891 in the European Nucleotide Archive. Scripts are available at https://github.com/chesQhub/barley_vernalisation_rnaseq. All predicted protein models are available at Dataset S1. © 2026 The Author(s). This is an open access article under the terms of the Creative Commons Attribution License., Flowering is controlled by environmental and genetic factors. Vernalization requirement inbarley (Hordeum vulgare L.) is determined by the allele in HvVRN1 and the presence of locusHvVRN2, which consists of two zinc-finger and CONSTANS-like domains (ZCCT) genes:HvVRN2a and HvVRN2b. While the effect of HvVRN2 presence is well known, its outcomeon the transcriptome and other genes outside the flowering/vernalization pathway remainsunknown. Near-isogenic lines, with presence/absence of HvVRN2, were subjected to vernalizationtreatments of different lengths, enabling the assessment of HvVRN2 expression dynamics aswell as broader transcriptional responses regulated by VRN2. Unknown differences in expression levels of the two HvVRN2 genes were identified, as wellas an effect on tillering. A regulatory network analysis pointed at new candidate genes forflowering regulation related to the vernalization pathway and suggested additional biologicalroles for HvVRN2b. Finally, protein modelling resulted in higher VRN2-Nuclear Factor-Y (NF-Y) stability than other CCT-NF-Y complexes. This study advances in the understanding of HvVRN2 in barley adaptation. The ZCCT geneswithin the HvVRN2 locus should be regarded as distinct genes and may possess broader adap-tive functions than previously recognized. Flowering repression by HvVRN2 may take place atthe protein level, potentially inhibiting formation of other CCT/NF-YB/NF-YC complexes thatactivate HvFT1 transcription., This work was supported by grants AGL2016-80967-R (AEI/10.13039/501100011033/FEDER/UE), PID2019-111621RB-I00 (AEI/10.13039/501100011033) and PID2022-142116OB-I00 (AEI/10.13039/501100011033/FEDER/UE). FM-T PhD was funded by the Government of Aragón, 2019-2023. FM-T three-month internship at John Innes Centre, under supervision of PB, was funded by a PhD mobility grant by the Government of Aragón., Peer reviewed

The Spanish Barley Core Collection (SBCC) is a source of genetic variability of potential interest for breeding, particularly for adaptation to Mediterranean environments. Two backcross populations (BC2F5) were developed using the elite cultivar Cierzo as the recurrent parent. The donor parents, namely SBCC042 and SBCC073, were selected from the SBCC lines due to their outstanding yield in drought environments. Flowering time, yield and drought-related traits were evaluated in two field trials in Zaragoza (Spain) during the 2014-15 and 2015-16 seasons and validated in the 2017-18 season. Two hundred sixty-four lines of each population were genotyped with the Barley lllumina iSelect 50k SNP chip. Genetic maps for each population were generated. The map for SBCC042 x Cierzo contains 12, 893 SNPs distributed in 9 linkage groups. The map for SBCC073 x Cierzo includes 12, 026 SNPs in 7 linkage groups. Both populations shared two QTL hotspots. There are QTLs for flowering time, thousand-kernel weight (TKW), and hectoliter weight on a segment of 23 Mb at similar to 515 Mb on chromosome 1H, which encompasses the HvFT3 gene. In both populations, flowering was accelerated by the landrace allele, which also increased the TKW. In the same region, better soil coverage was contributed by SBCC042 but coincident with a lower hectoliter weight. The second large hotspot was on chromosome 6H and contained QTLs with wide intervals for grain yield, plant height and TKW. Landrace alleles contributed to increased plant height and TKW and reduced grain yield. Only SBCC042 contributed favorable alleles for "green area, " with three significant QTLs that increased ground coverage after winter, which might be exploited as an adaptive trait of this landrace. Some genes of interest found in or very close to the peaks of the QTLs are highlighted. Strategies to deploy the QTLs found for breeding and pre-breeding are proposed.

Early vigor has been proposed as a favorable trait for cereals grown in drought-prone environments. This research aimed at characterizing early stage shoot and root growth of three Spanish barley landraces compared with three modern cultivars. Genotypes were grown in an automated phenotyping platform, GrowScreen-Rhizo, under well-watered and drought conditions. Seminal and lateral root length, root system width and depth were recorded automatically during the experiment. Drought induced greater growth reduction in shoots (43% dry weight reduction) than in roots (23% dry weight). Genotypic differences were larger under no stress, partly due to a more profuse growth of landraces in this treatment. Accession SBCC146 was the most vigorous for shoot growth, whereas SBCC073 diverted more assimilates to root growth. Among cultivars, Cierzo was the most vigorous one and Scarlett had the least root dry weight of all genotypes, under both conditions. Root growth was redirected to lateral roots when seminal roots could not progress further in dry soil. This study reveals the presence of genetic diversity in dynamics of early growth of barley. The different patterns of growth observed for SBCC073 and SBCC146 should be explored further, to test if they affect field performance of barley in drought-prone environments.

Roots are important for crop adaptation, particularly in dryland environments. We evaluated root development of 37 durum wheat genotypes (modern cultivars and landraces) in the field at the adult plant stage, through a shovelomics approach. Large genotypic variability was found for root traits. Differences between the landraces and modern cultivars were the main driver of this variation, with landraces showing higher plant vigor for roots and shoots. Nonetheless, genotypic variation within groups was also observed, related to different models of root growth, largely independent of total root length. These two models represented root growth were oriented either to occupy more soil volume, or to occupy less soil volume with increased density. The field results were then compared with root data previously collected in seedlings using a filter paper-based method, to assess whether early root anticipated adult root features. Field plants showed a narrower root angle than seedlings. In particular, landraces presented a narrower root angle than cultivars, but only at seedling stage. Potentially useful correlations were found between the two growth stages for root length and number. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant’s response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka × Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL co-locating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley., info:eu-repo/semantics/publishedVersion

Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant’s response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka × Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL co-locating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley., info:eu-repo/semantics/publishedVersion